I don't think there's a wrong answer here. Your runner chose you just like your runner chose his/her footwear. It was your runners choice and can really only be answered by them. I say good for you for being there for your runner and wrestling with the decision...
That said, I really like screwing with a 3am, 80 mile runner's head. They are pretty gullible and will play along with just about any old tired bit. If they take issue the next morning, I just tell them about the great hallucination they had...
Please don't second guess yourself...you were there for your runner and you used your best judgement when theirs was diminished. You did your job.

""...the truth that someday, you will go for your last run. But not today—today you got to run." - Matt Crownover (after Western States)

When I was communicating with my pacers in the weeks before my Pinhoti 100 race, I gave them specific details about what to expect from me and about how to talk me through those moments. I told them that I was trying to think everything through in detail before the race, because I might not be able to think much at all during the actual race. All that I really expected out of my pacers was another voice a few feet behind me on the dark trails in the middle of the night, but I also told them not to be afraid to put their hands on my shoulders, look me in the eye, and tell me that I was going too slow to meet cutoff times. Thankfully, I stayed well ahead of cutoff times during the race, but I would have certainly appreciated some forceful words and a fire under my tail if I had been in danger of being pulled.